We have worked with many high-throughput datasets including the data generated by NCI investigators and those from public domains. In particular, we have worked with a series of mouse mammary tumor models with the data generated by many NCI investigators. The data span many platforms including whole genome sequencing, exome sequencing, RNAseq, DHS, ChIP-seq, bisulfite-sequencing, ChIA-PET, RIP-seq, RPPA, metabolomics, and involve multiple tissues, primary tumors and lung metastasis. We are currently doing integrated analyses, including integrating sequence variants with DHS and gene expression; integrating methylation with gene expression and genome sequence features; integrating gene expression with therapeutic response data. Similarly, we have also conducted integrated analyses for TCGA data, involving collaborations with many NCI investigators. We are also developing computational methods to empower the data analyses.